est_amplification_efficiency {WES}

Estimate PCR amplification efficiency

Description

This function takes a set of serial diluted concentrations of target nucleic acid from a standard curve assay and their associated Ct values and estimates the percentile amplification efficiency using a linear model as described in Yuan et al. (2008). Note that the model uses a log base 2 transform which assumes that serial dilutions double with each increase in concentration. The function also requires a minimum of 5 observations.

Usage

est_amplification_efficiency(n_copies, ct_value)

Arguments

n_copies

A numeric vector giving the serial diluted concentration of target nucleic acid

ct_value

A numeric vector giving the measured Ct value for each serial dilution in the standard curve design

Value

List containing the mean, and low and high of the 95% confidence interval for the percentile amplification efficiency.

Examples

sel <- template_WES_standard_curve$target_name == 'target_1'
tmp_n_copies <- template_WES_standard_curve$n_copies[sel]
tmp_ct_value <- template_WES_standard_curve$ct_value[sel]

est_amplification_efficiency(n_copies = tmp_n_copies,
                             ct_value = tmp_ct_value)